#
#	HMM-GRASPx: guided search and assembly of short peptides using HMM models
#
#	Please direct comments, suggestions, bug-reports to Cuncong Zhong (czhong@jcvi.org)
#

1: Runing individual programs
	
	* 'graspxp-build' is used to construct the index. Assuming that you are under directory
	  '/HMMGRASPx_home/', simply type './bin/graspxp-build ./Examples/mix3fams.fa'. The build
	  program will create a set of indexing files and put into '/HMMGRASPx_home/WorkSpace'.

	* 'graspxp-assemble' is used to perform targeted assembly. Assuming that you are under 
	  directory '/HMMGRASPx_home/', and that you have finished the previous building step, 
	  simply type 
	  './bin/graspxp-assemble ./Examples/mix3fams.hmm ./Examples/mix3fams.fa raw_contigs.fa'.
	  The program will generate file 'raw_contigs.fa', which is in the FASTA format and contains
	  all contigs being assembled in this stage.

	* 'graspxp-map' is used to align the short peptides against the assembled contigs. Assuming
	  that you are under directory '/HMMGRASPx_home/', and that you have finished the previous
	  assembly step, simply type
	  './bin/graspxp-map ./Examples/mix3fams.fa raw_contigs.fa mapping.list'.
	  
	  IMPORTANT: Note that this step will directly mapping short peptides against the raw contigs
	  generated from the previous step. We suggest that the raw contigs being first verified by
	  HMMER3 re-alignment (e.g. between './Examples/mixfams.hmm' and 'raw_contigs.fa') before donig
	  the mapping. This step is optional but important in reducing false-positive predictions.
	  Below you will find the use of a driver script that automatically include the verification 
	  process.

	  The resulting mapping output is a table that contains three fields, namely 1: the ID of the
	  read in the data set; 2: the header/name of the read; and 3: the header/name of the contig
	  where the read is mapped onto.
 
2: Using the "RunHMMGRASPx.pl" script to streamline your analysis

	* The script requires HMMER3 (http://hmmer.janelia.org/). This current release should 
	  contain a copy of the software under the '/HMMGRASPx_home/ThirdParty' folder.
	* You need to compile HMMER3. First go to '/HMMGRASPx_home/ThirdParty/hmmer-3', and
 	  then type './configure'.
	* In the same directory, type './make'. If the compilation is successful, you should
	  find that all executables have been put under directory 
	  '/HMMGRASPx_home/ThirdParty/hmmer-3/binaries'.

	* After compiling HMMER3, you should be able to use the "RunHMMGRASPx.pl" script. To
	  analyze the data given in '/HMMGRASPx_home/Examples', simply type (assume you are under
	  /HMMGRASPx_home/)
	  'perl Scripts/RunHMMGRASPx.pl --hmm=Examples/mix3fams.hmm --seq=Examples/mix3fams.fa --out=TestResults --home=./ --index=WorkSpace/ --param=Settings/param'

	* To find out meaning of the options, please type 'perl Scripts/RunHMMGRASPx.pl'